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Knowledge Exchange Workshop: Practical Solutions with Ontologies | BioMedBridges

Knowledge Exchange Workshop: Practical Solutions with Ontologies

This workshop was held at the EMBL-EBI on the 4-5 March 2013.
For more information about the event, please contact Tom Hancocks -

Workshop Overview

This workshop introduced several widely used ontologies for the life sciences. It familiarized participants with approaches to using these ontologies for data curation and integration. The content covered the role of ontologies in the wider framework of interoperability, such as the semantic web framework and the use of RDF to describe data. BioMedBridges partners presented use cases to illustrate both proven and experimental approaches to annotating biomedical data by combining existing ontologies on an 'as needs' basis. The workshop combined presentations, discussions and hands-on experience of using established approaches, encouraging participants to consider how to resolve common data sharing and integration problems within the BioMedBridges project. All partificpants contributed towards the creation of a 'living document' on ontologies to facilitate ongoing work throughout the BioMedBridges project.

Ontology Resources

The following pages contain useful information taken from the Living Document

Ontologies: Starting Out

Ontologies: Expertise

Ontologies: Technology

Ontologies: for BioMedBridges

Ontologies: FAQ

Ontologies: Participants

Ontologies: 'Things'


Time Topic Speaker
Day 1 - 4 March 2013
09:30 Welcome and introduction Tom Hancocks, BioMedBridges
10:00 Introduction to ontologies in the life sciences Robert Stevens, University of Manchester
10:30 Break  
11:00 Current ontology landscape Robert Stevens, University of Manchester & James Malone, EMBL-EBI
12:00 Participant slides Robert Stevens, University of Manchester & James Malone, EMBL-EBI
12:30 Lunch  
13:30 Technology overview Simon Jupp & James Malone, EMBL-EBI
15:00 Break  
15:30 Discussion session: delegate requirements Tom Hancocks, BioMedBridges
18:30 Workshop Dinner  
Day 2 - 5 March 2013
09:30 BMB use cases overview:
* ArrayExpress and EFO
* KupKB 
* Ontology use by the IMPC
James Malone, EMBL-EBI
Simon Jupp, EMBL-EBI /Robert Stevens, University of Manchester
Terry Meehan, EMBL-EBI
11:00 Break  
11:30 BMB use cases overview:
* Use of Ontologies in Instruct/PiMS 
* Systems microscopy; EuBi cellular phenotype ontology
Chris Morris, STFC
Gabriella Rustici, EMBL-EBI
12:30 Lunch  
13:30 The role of RDF and the semantic web James Malone, EMBL-EBI
15:00 Break  
15:30 Discussion session: FAQ development Tom Hancocks, BioMedBridges 
17:00 Wrap up and evaluation  Tom Hancocks, BioMedBridges  
17:30 End of workshop  

Living Document

The Living Document created during the course can be viewed as a Google Doc: Practical Solutions with Ontologies



The slides used as part of the workshop have been uploaded onto this webpage for reference.